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In considering the history of biodiversity paleontologists have focused on exploratory investigations of empirical data derived from the fossil record. Starting with the pioneering work of Philips (1860), and continuing at an increasing pace through today, this inductive approach has dominated diversity research. In contrast, deductive theoretical considerations that focus on the expected history of biodiversity, and develop independently of empirical knowledge, have remained under-explored. Appreciating the need for a nomothetic paleobiology (Gould 1980), we here reconsider the history of biodiversity, using deductive models constrained by a few, self-evident parameters. This analysis centers on the marine fossil record, the primary target of most previous empirical studies on the geological history of global biodiversity (e.g., Valentine 1969; Raup 1972, 1976; Sepkoski et al. 1981; Alroy et al. 2008).

This paper presents a method for constraining the age of a clade with the ages of the earliest fossil specimens in that clade's outgroups. Given a sufficiently deep, robust, well-resolved, and stratigraphically consistent cladogram, this method can yield useful age constraints even in the absence of specific information about the fossil preservation and recovery rates of individual taxa. The algorithm is applied to simulated data sets to demonstrate that this method can yield robust constraints of clade ages if there are sufficient fossil outgroups available and if there is a finite chance that additional outgroups may be discovered in the future. Finally, the technique is applied to actual fossil data to explore the origin of modern placental mammals. Using data from recently published cladograms, this method indicates that if all Mesozoic eutherians are regarded as outgroups of Placentalia, then the last common ancestor of modern placental mammals and their Cenozoic allies lived between 65 and 88–98 million years ago, depending on the assumed cladogram and the number of outgroups included in the analysis.

Fundamental to the interpretation of bone-bearing faunal deposits is an understanding of the taphonomic processes that have modified the once living fossil community. An often neglected source of bias is that of climate-averaging, which occurs when the duration of bone accumulation exceeds the duration of an individual climatic episode. Tropical and subtropical climate change is dominated by precessional cyclicity (~21,000 year cycle), which controls monsoon rainfall intensity and thus plant communities over time. Under a climate-averaging scenario, the paleoecological characteristics of a faunal deposit represent an amalgamation of more than one phase of the precessional cycle. We investigate the degree of climate-averaging in Plio-Pleistocene bone breccias from South Africa by comparing stable isotope measurements of fossil enamel with the evidence from high-resolution speleothem paleoclimate proxies. We conclude that each of the four faunal assemblages studied are climate-averaged, having formed over a time period in excess of one-third of a precessional cycle (~7000 years). This has implications for the reconstruction of hominin paleoenvironments and estimates of Plio-Pleistocene biodiversity. We hypothesize that climate-averaging may be a common feature of tropical terrestrial vertebrate assemblages throughout the Cenozoic and Mesozoic.

Did organisms diversify in different ways on land and in the marine realm over the Phanerozoic, or do the different diversification curves of continental and marine organisms reflect primarily methodological artifacts? To answer this question, a quantitative assessment of the completeness of the global continental fossil record is indispensable. We used comparisons between continental and marine fossil diversity and between past and present-day patterns of continental diversity to assess the absolute and relative completeness of the continental fossil record. Collector's curves of the number of described families over the past 200 years suggest that the global continental fossil record, and even that of European and North American tetrapods, is still highly incomplete. Nevertheless, relative proportions of major continental and marine taxa, patterns of tetrapod endemism, and familial durations suggest that the family-level continental fossil record is reasonably representative. We found that, although continental fossil richness is correlated with the amount of terrestrial clastic sediment available for sampling, the exponential diversification curve of continental metazoans is unlikely to be an artifact of this rock bias. Diversification of the continental fauna appears to have been essentially exponential since the Devonian, with little evidence of major extinction events.

A growing body of work has quantitatively linked many macroevolutionary patterns, including short- and long-term changes in biodiversity, rates of taxonomic extinction and origination, and patterns of extinction selectivity, to temporal variability in the sedimentary rock record. Here we establish a new framework for more rigorously testing alternative hypotheses for these and many other results by documenting the large-scale spatiotemporal intersection of the North American sedimentary rock and fossil records. To do this, we combined 30,387 fossil collections in the spatially explicit Paleobiology Database with a comprehensive macrostratigraphic database consisting of 18,815 sedimentary lithostratigraphic units compiled from 814 geographic regions distributed across the United States and Canada. The geological completeness of paleontological sampling, here defined as the proportion of the available sedimentary rock record that has been documented to have at least one fossil occurrence, irrespective of taxonomy or environment, is measured at four different levels of stratigraphic resolution: (1) lithostratigraphic rock units, (2) hiatus-bound rock packages, (3) regional stratigraphic columns, and (4) sediment coverage area (km2). Mean completeness estimates for 86 Phanerozoic time intervals (approximately stages; median duration 5.3 Myr) range from 0.18 per interval in the case of lithostratigraphic rock units to 0.23 per interval for stratigraphic columns and sediment coverage area. Completeness estimates at all four levels of stratigraphic resolution exhibit similar temporal variation, including a significant long-term increase during the Phanerozoic that is accentuated by an abrupt Campanian–Maastrichtian peak. This Late Cretaceous peak in completeness is approximately five times greater than the least complete Phanerozoic time intervals (Early Cambrian, Early Devonian, late Permian, and Early Cretaceous). Geological completeness in the Cenozoic is, on average, approximately 40% greater than in the Paleozoic. Temporal patterns of geological completeness do not appear to be controlled exclusively by variation in the frequency of subsurface rock units or an increase over time in the proportion of terrestrial rock, but instead may be general features of both the marine and terrestrial fossil records.

Microfossil bonebeds are multi-individual accumulations of disarticulated and dissociated vertebrate hardparts dominated by elements in the millimeter to centimeter size range (≤75% of bioclasts ≤5 cm maximum dimension). Modes of accumulation are often difficult to decipher from reports in the literature, although predatory (scatological) and fluvial/hydraulic origins are typically proposed. We studied the sedimentology and taphonomy of 27 microfossil bonebeds in the Campanian Judith River Formation of Montana in order to reconstruct formative histories. Sixteen of the bonebeds examined are hosted by fine-grained facies that accumulated in low-energy aquatic settings (pond/lake microfossil bonebeds). Eleven of the bonebeds are embedded in sandstones that accumulated in ancient fluvial settings (channel-hosted microfossil bonebeds). In lieu of invoking separate pathways to accumulation based on facies distinctions, we present a model that links the accumulation of bioclasts in the two facies. We propose that vertebrate material initially accumulates to fossiliferous levels in ponds/lakes and is later reworked and redeposited as channel-hosted assemblages. This interpretation is grounded in reasonable expectations of lacustrine and fluvial depositional systems and supported by taphonomic data. Moreover, it is consistent with faunal data that indicate that channel-hosted assemblages and pond/lake assemblages are similar with regard to presence/absence and rank-order abundance of taxa.

This revised model of bonebed formation has significant implications for studies of vertebrate paleoecology that hinge on analyses of faunal data recovered from vertebrate microfossil assemblages. Pond/lake microfossil bonebeds in the Judith River record are preserved in situ at the scale of the local paleoenvironment, with no indication of postmortem transport into or out of the life habitat. Moreover, they are time-averaged samples of their source communities, which increases the likelihood of capturing both ecologically abundant species and more rare or transient members of the paleocommunity. These attributes make pond/lake microfossil bonebeds excellent targets for paleoecological studies that seek to reconstruct overall community membership and structure. In contrast, channel-hosted microfossil bonebeds in the Judith River record are out of place from a paleoenvironmental perspective because they are reworked from preexisting pond/lake assemblages and redeposited in younger channel facies. However, despite a history of exhumation and redeposition, channel-hosted microfossil bonebeds are preserved in relatively close spatial proximity to original source beds. This taphonomic reconstruction is counter to the commonly held view that microfossil bonebeds are biased samples that have experienced long-distance transport and significant hydrodynamic sorting.

A large sample of the Pikermi and Samos ungulates was examined by microwear analysis using a light stereomicroscope (561 extinct and 809 extant comparative specimens). The results were used to infer the dietary adaptations of individual species and to evaluate the Pikermian Biome ungulate fauna. Many of the bovids have wear consistent with mixed feeding, although a few mesodont taxa apparently enjoyed an exclusive browsing and or grazing diet. The giraffids spanned the entire dietary spectrum of browsing, mixed feeding, and grazing, but most of the three-toed horses (Hippotherium) were hypsodont grazers. The colobine monkey Mesopithecus pentelici displays microwear consistent with a mixed fruit and leaf diet most likely including some hard objects. Similar results were obtained from prior scanning electron microscopy microwear studies at 500 times magnification and from the light microscope method at 35 times magnification for the same species. Results show that diet can differ between species that have very similar gross tooth morphology. Our results also suggest that the Pikermian Biome was most likely a woodland mosaic that provided a diversity of opportunities for species that depended on browsing as well as species that ate grass. The grasses were most likely C3 grasses that would grow in shaded areas of the woodland, glades, and margins of water. The ungulate component of the Pikermi and Samos fauna was more species-rich and more diverse in diet than the ungulates observed in modern African forests, woodlands, or savannas, yet dietarily most similar to the ungulates found in woodland elements of India and to some extent of Africa. It is unlikely that the Pikermi and Samos ungulates inhabited dense forests because we find no evidence for heavy fruit browsing. Conversely, a pure savanna is unlikely because many mixed feeders are present as well as browsers. Extant woodland African species are morphologically and trophically very similar to the African savanna species. Therefore the evolution of grazing and of hypsodont morphology for Africa may have evolved within the Plio-Pleistocene woodlands of Africa. Our results show that major dietary and morphologic ungulate evolution may take place within woodlands rather than as a consequence of species moving into savannas both during the late Miocene of Pikermi and Samos and during the Pleistocene–Recent of Central Africa.

Natural accumulations of skeletal remains represent a valuable source of ecological data for paleontologists and neontologists alike. Use of these records requires a quantitative assessment of the degree to which potential biasing factors affect how accurately ecological information from the living community is recorded in the sedimentary record. This has been a major focus in recent years for taphonomists working with marine records, yet terrestrial systems have remained virtually unstudied—particularly communities of small-bodied taxa. Our ability to assess the potential origins and effects of postmortem bias in terrestrial skeletal assemblages (both modern and fossil) has therefore been limited. Predation is a common mechanism by which small-mammal skeletal remains are concentrated; raptors regurgitate the remains of their small-mammal prey in pellets rich in skeletal material, which accumulate below long-term roosting sites, especially in protected areas such as caves and rock shelters. Here I compare small-mammal death assemblages concentrated via owl predation at Two Ledges Chamber, a long-term owl cave roost in northwestern Nevada, with data from modern trapping surveys to evaluate (1) their ecological fidelity to the modern small-mammal community, (2) the effects of temporal variation and time-averaging (over months to centuries) on live-dead agreement, and (3) how spatial averaging affects the landscape-scale picture of the small-mammal community as reconstructed from dead remains. Despite potential obstacles to the recovery of ecological information from skeletal deposits generated via predation, I find high live-dead agreement across all ecological metrics and all temporal comparisons. I also find that the effects of time-averaging (specifically increased species richness of the death assemblage) become significant only at the century scale. Finally, I combine a mixing model approach with a principal coordinates analysis to show that the owls at Two Ledges Chamber sample from all habitats present in the immediate vicinity of the cave, producing a high-fidelity snapshot of the community that is spatially integrated at the local landscape scale.